4. Environment Set-up

4.1 Create a suitable environment

This is the main environment used in the repository.

python3.11 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt
pip install -r requirements_docs.txt

Note that a separate Python 3.9 environment is required to run the scispacy notebooks:

python3.9 -m venv .venv_scispacy
source .venv_scispacy/bin/activate
pip install -r requirements_scispacy.txt

This repo uses pre-commit to ensure black and flake8 has been applied. You will need to make sure your virtual environment has been activated.

source .venv/bin/activate
pre-commit install